Naruto and the New World
by The Rapping Kage
Summary: Its dark times after the Fourth Great Ninja War. Naruto finds out about the truth of his mother's village's destruction and chooses a side. Sasuke sacrifices his life and eyes for Naruto.Teaming up with the Akatsuki temporarily. Naru/FemItachi/Konan
1. Chapter 1

It is a dark time for the world. Buildings crushed, ground littered with forgotten kunai. Innocent lives were ruined, and it all happened in a short period of time. Dead bodies could be found on the roads between villages that used to be bright and attractive to travelers. Those who survived were not concerned though. The aftermath of the Fourth Great Ninja War left scars across the world.

It all started with the assassination of the Third Hokage of Konoha. The culprit left behind an Iwa headband and a taunting note. The citizens of Konoha were in an uproar, an opportunity a certain war-hawk couldn't pass up. Danzo Shimura quickly took up the position of Hokage and began preparations for a declaration of war against Iwagakure. Before war could break out, a convening of the five kages was called together. At this meeting, Danzo blatantly blamed the Tsuchikage for the murder of Konoha's beloved professor. Naturally, he didn't take that well and declared war upon Konoha, much to the protests of the other three kages: Mei Terumi the Fifth Mizukage, A the Fourth Raikage, and Gaara the Fifth Kazekage. Unknown to the bickering kages, a man with a spiral mask watch the seen with a maniacal gleam in his one revealed eye. The Fourth Great Ninja War had begun. Kiri and Suna allied themselves with Konoha, while Kumo and Iwa teamed up.

It wasn't long before the bijuu came in to play. Naruto was called back to the village to serve, interrupting his training trip with Jiraiya. It also had appeared that the Akatsuki had teamed up with Iwa and Kumo in exchange for their Jinchuuriki. The two sides appeared to be evenly matched until the Akatsuki managed to capture Naruto. Danzo had immediately organized a search and rescue party, he couldn't lose his most valuable tool after all. The team consisted of Jiraiya, Kakashi, Sai, and Sakura. However, as the rescue team was chasing after Naruto, Pain and Konan attacked Konoha. Without their best shinobi around, the village was eradicated beneath the power of the Rinnegan's Shinra Tensei. But Danzo was not idle during this time. He sacrificed himself to kill Pain by unleashing the power of all his Sharingan eyes and Mokuton powers to erupt a forest of unparalleled power, beyond that of even the First Hokage, and trapped himself and all of Pain's bodies into it, stuck in a Sharingan-induced Genjutsu forever. But Danzo's victory was only short. Konan had came and killed Danzo while he was stuck in the genjutsu and retrieved Pain's main body.

The rescue team had eventually reached the Akatsuki members and were shocked at what they saw. Naruto was in an Akatsuki cloak along with Sasuke and Itachi. But the team was shocked at the appearance of Itachi. It wasn't the fact that he was alive, it was the fact that he was actually a she! Itachi explained how she had to pretend to be a male so she could be the heir to the Uchiha clan while Naruto glared intensely at the team. When they questioned why he betrayed them, he muttered with barely constrained anger about how the village hid the identities of his parents from them and how the Third had orchestrated the destruction of his mother's village. The battle soon commenced, and Sakura was taken out within the first minute. It was one of the most intense battles the ninja world has ever seen, right next to Hashirama and Madara's battle. Sai also fell after 5 minutes of barely holding up. Soon it was just Jiraiya and Kakashi against the Akatsuki trio. Jiraiya unleashed his sage mode and Kakashi uncovered his Mangekyo Sharingan eye.

"Give it up Ero-Sennin, Kakashi-sensei." Naruto said coldly. Itachi and Sasuke were coming up to flank them.

"Too late Naruto!" Jiraiya suddenly appeared next to Naruto with an Ultimate Oodama Rasengan ready to plunge into his chest.

Naruto's eyes widened in fear, along with Sasuke's and Itachi's. Suddenly Sasuke appeared in Naruto's place and he had his eyes closed, as if in peace with his decision. "Sasuke!" Naruto screamed out tears coming out of his eyes as red chakra started to seep out of him. Sasuke's unmoving body laid on the ground, his cloak in tatters. Naruto charged at Jiraiya and Jiraiya smirked pulling out a demon chakra suppressing seal and slammed it on Naruto.

"**Not this time, foolish mortal"** Naruto/Kyuubi growled out and separated Jiraiya's head from his shoulders with a swipe of his claws.

He looked over for his other victim and saw Kakashi on the ground, dead, with blood pouring out of his body, Itachi standing over him.

"Na..ru…to…"

He could hear coming from Sasuke's body. Naruto calmed down instantly and ran to his best friend's side.

"Naruto…take..my eyes.." Sasuke mumbled.

Naruto froze, shocked at his friend's sacrifice.

"I can't Sasuke, you need them!" Naruto exclaimed.

"Dobe…I'm dying..just take them and.. ensure Konoha's destruction for.. me." Sasuke stated, drawing his last breath.

Naruto started sobbing as Itachi came over to Sasuke's body, taking the eyes carefully from her beloved brother.

"Rest in peace, dear brother... I will make sure your eyes are put to good use" she said, shedding a tear before pausing after taking the first eye. She looked over to Kakashi's dead body and walked over before taking his Mangekyo eye with a cold look. She then turned to Naruto and knocked him out then proceeding to implant Kakashi's eye and Sasuke's eye onto Naruto. After she finished the transplant, she burned the bodies of all the deceased ninja except Sasuke. She picked up Naruto's body and laid a kiss on his forehead and carried his body bridal style towards the horizon at top speed.

**END**

**Wow, feels like I created an entire new universe o_O going to be hard to keep up with all the new changes. Review or pm with any questions not involving me revealing the new content upcoming in the new chapters I have planned and I will answer to the best of my abilities.**


	2. Chapter 2

**So yeah, tried to update as quickly as possible. Thanks for the reviews and questions. Now I've had some questions concerning the Third Hokage and how he was still alive during that time period. The answer is that during the Sand/Sound invasion, the Third did not use the Shiki Fujin to force Orochimaru to flee, instead not allowing any of the Hokages to be resurrected and beating him pretty soundly(no pun intended). He then lived for a while until he was assassinated. Anyway, on to the story.**

_**Three years after Naruto's betrayal**_

Naruto stood across his enemy, observing his every movement and anticipating his next move.

"Zetsu…now that I have found your main body…its your turn to die." Naruto said calmly.

Zetsu's eyes widened in fear as he attempted to sink underground but a yellow flash caught the venus flytrap and pulled him back up.

"Y..You know the Hiraishin?" cried out the plant man as he winced at the feeling of the tip of his plant/head being squeezed by Naruto's intense strength.

"Die." Naruto stated simply and pulled out a wakizashi and stabbed it through Zetsu's head. He then teleported to his left as a kunai missed his head barely, another Zetsu coming out from behind a tree. However, another Naruto came out from the same spot and cleanly sliced Zetsu's head off before incinerating him with a fireball. _Too easy, _Naruto thought, _that's why he was a spy, not much combat capabilities. Oops can't believe I almost forgot this." _Naruto thought as he bent down, picking up a shiny ring from the dust of Zetsu's body. He wordlessly dispelled his clone and started walking towards his next destination. "_Only one more ring to go,_ he thought, looking down at his hands and the 9 rings on his hands. _I wonder how Itachi-chan and Konan-chan are doing._ He thought before shrugging to himself.

"I guess a little break couldn't hurt." He then used the Hiraishin and disappeared.

Meanwhile, somewhere between Kumo and Iwa, a fierce battle was going on between Jinchuuriki.

"Damnit.. they're strong Bee." A blond haired kunoichi said to a tanned man with sunglasses.

"Don't worry Yugito, they ain't no match for the king yo!" The now named Bee responded with a little dance as a reddish chakra started coming off of him. Yugito face-palmed, calling forth her demon chakra as well.

The Iwa Jinchuuriki, named Roshi and Han, did not even speak, just rushed toward their mission objective, Kumogakure. Their mission: to destroy Kumogakure after the Kumo ninjas betrayed them. The village of Iwa was in rubble after the Raikage and his brother Bee went loose and destroyed their rocky counterparts.

"Where those fools think they goin'? I was just startin' to get my juices flowin'!" Bee growled out.

"**Couldn't you make that buffoon stop talking like that kitten?"** The Nibi spat out in annoyance of the rapping jonin.

"You know I've tried Nibi, he just won't stop!" Yugito exclaimed in frustration.

"C'mon girly we've fallen too far behind, if something happens our asses will be put on the grind!"

Yugito just mumbled before following Bee. After several minutes of high speed running, Bee came to a sudden stop and she ran straight into him.

"What's your problem Bee!" Yugito yelled. Bee just stood with a grim look on his face and pointed in the direction of the village.

"What are you pointing..at…Oh my god! What the hell happened? We couldn't have fallen that far behind them! Yugito cried, tears cascading down her beautiful face. The village was in ruins. Dead bodies were strewn about the streets and the Kage tower, which could be seen in the distance, looked like it had been ripped in half and was on fire.

They headed toward the tower, hoping to find the Raikage and any other survivors. As they reached the new "top" of the tower, they saw something disturbing. The Raikage was dead, but he wasn't alone. The Tsuchikage and Han also lay dead. Yugito and Bee quickly went over to the Raikage and checked his pulse and their hearts clenched as there was none. Bee let out a guttural scream of intense emotional pain as he mourned the loss of his brother with Yugito crying next to him. It appeared that they were the last two survivors of their village.

"It seems you two have learned the cost of betrayal.."

Yugito and Bee's heads quickly snapped in the direction of the voice. Their eyes widened as they saw the spiral mask and the spinning tomoe.

**END**

**So, let me know what you think about this chapter. I plan on having a short selection of actual "main" characters and Yugito and Bee will be central to the storyline I have planned. Once again, feel free to review or pm any questions you might have that don't involve revealing anything from future chapters.**


	3. Chapter 3

**Hey guys! This is the last of the "short" chapters. After this, I'm going for 5k+ words a chapter, so expect a little longer delay between updates.**

_**Last chapter..**_

"_**It seems you two have learned the cost of betrayal.."**_

_**Yugito and Bee's heads quickly snapped in the direction of the voice. Their eyes widened as they saw the spiral mask and the spinning tomoe.**_

"You! What do you want? You are the cause of all of this!" Yugito vented onto the masked man.

"I am merely the engineer who starts the gears turning, whatever happens after that is of your own accord." The masked man spoke calmly.

"Bull shit! You're the one who sparked this whole war, and forced us to betray Iwa!" She shouted.

Suddenly, Bee came out from behind the masked man and lunged. "Enough of this! You done got me pissed!" Bee roared. But the masked man just smirked, unknowingly to the other two, as Bee just went through his body.

"I can't kill you because I need you for my plans so…"

"Like you could kill us any.." Yugito broke off. The masked man's smirk just grew wider as she came under his control.

"Yugito, what you doin' just standin there yo?" Bee questioned.

She didn't say anything however and lunged at him, causing him to backflip and land right in front of the masked man, making eye contact with his spinning Sharingan tomoe. The Hachibi tried to fight off the influence of the genjutsu, but slowly, both bijuu and container succumbed to the genjutsu.

"Hmm…seems you two are under my control for now. So for now go to Amegakure and see if you can capture the Kyuubi jinchuuriki and kill the traitors." The masked man ordered the Kumo jinchuuriki.

Yugito and Bee nodded in response and with a small puff of smoke disappeared to complete their mission.

Meanwhile, Naruto was in the process of teleporting between Hiraishin seals on his way to Amegakure. He was reminiscing about the takeover of the Akatsuki.

_**Shortly after Naruto woke up after a good night's sleep caused by another one of Itachi and Konan's training sessions, the both of them appeared in front of Naruto. **_

"**Naruto-kun, it is time we begin the rebellion against the masked man and the other members of Akatsuki." Konan told him.**

"**I see…do you believe I am at a high enough level of power already?" He questioned with a twinge of nervousness.**

"**Naruto-kun, you've already surpassed the both of us combined." Itachi stated bluntly with a small smirk as Konan plopped down on Naruto's lap.**

**Naruto blushed slightly before coming serious again. "Do you think its time for me to get one of his eyes then? I think that's the only way that I can defeat the masked man without abusing the Kyuubi's power, which could prove disastrous if you two were around" he finished softly.**

**Konan smiled sadly before nodding. "Nagato would have wanted you to use the power of Rikudo Sennin for peace." **

**Naruto nodded with a small smile before getting up off his bed bringing Konan up with him bridal style, causing her to yelp slightly. **

"**Alright..let's head off for that eye then, Kakashi's felt wrong to me but Sasuke's is okay." He stated solemnly. Both girls nodded and Itachi wrapped her arms around Naruto as they disappeared in a yellow flash.**

**Later that day, during a meeting of the remaining Akatsuki members(All except Konan and Itachi are still alive) a yellow flash appeared on top of the statue. Everyone's heads immediately snapped there and their eyes widened as one of the topics of their meeting was standing right there confidently with the two traitors right next to him.**

"**You must be pretty confident boy, to show yourself hear with only those two as backup." Kakuzu commented. The masked man narrowed his eyes at Naruto seeing an illusion around his eyes and dispelled it. His single showing eye widened to epic proportions and he instantly teleported away, leaving the rest of the Akatsuki to deal with them. Naruto flashed off after him.**

"**Where'd that creepy leader of ours go off to?" Hidan questioned.**

"**He must have known that we would be able to stop these three so he didn't want to waste any of his time" Sasori commented quietly. After that was said, they all charged at the three intruders. Naruto smirked as six bodies suddenly appeared with piercings. The Akatsuki members trembled with fear at who they were up against. Not only did it appear Naruto had the Rinnegan AND Sharingan, but he was controlling some of the most renown ninja in the history of the shinobi era. These paths were the First Hokage, Second Hokage, Fourth Hokage, Madara Uchiha, Sasuke Uchiha, and Kushina Uzumaki. The paths were making quick work of the Akatsuki shinobi. Kisame and Sasori had already fallen to the combined teamwork of the resurrected Uchihas. The remaining members soon realized that they couldn't win the fight and fled, leaving the paths, Itachi, and Konan to go after Naruto to assist him after collecting the fallen's rings.**

**In a forest, the masked man suddenly appeared, panicking at the fact that somebody had achieved what his goal was, to obtain both the Rinnegan and the Sharingan. His eyes widened as a flash crossed in front of him and punched him right in the face. **

"**Your day of reckoning has come, Tobi." Naruto stated with an air of power about him. **

**Suddenly the orange spiral-masked shinobi came out and yelled with an obnoxious voice "How did you discover my name?" Naruto simply raised a brow and the masked man, now known as Tobi, went back to normal.**

"**Darn, was hoping that would catch you off guard." Tobi stated.**

"**Didn't work out very well." A voice came from behind him. Tobi tried to turn intangible but was not quick enough and a sword cleaved through his left arm as Tobi teleported away, the bloody arm laying on the ground.**

"**Damnit he got away" Naruto grumbled. He checked the arm to see if it was the one with his ring on it and got frustrated because it wasn't the one. Itachi, Konan, and the paths came upon this sight.**

"**He got away Naruto-kun?" Itachi observed. **

**Naruto nodded."Let's head home girls." He stated and the paths disappeared with puffs of smoke as Naruto grabbed the girls and flashed back to his room in Amegakure's kage tower. **

**Over time, Naruto meticulously hunted down the other Akatsuki members. One year later, he only had one left…the one who escaped and the most dangerous of them all.**

Naruto remembered that day well, it was the day he transcended from a normal shinobi, a normal jinchuuriki even, and became as powerful as a descendant of the Rikudo Sennin. He soon reached the gates of Amegakure and was suddenly confronted by two ninja.

"Can I help you with something pretty lady?" Naruto asked with a raised eyebrow to the female of the two, completely disregarding the tanned man with many swords on his back.

"Naruto Uzumaki?" Yugito asked. Naruto nodded, brow still raised. Bee got into a stance and Yugito stated, dronelike, "We must terminate you for our master."

Thus began the battle between the fox, cat, and ox-topus.

**END**

**Thought this chapter turned out pretty good, introduced the beginning of the end of the Akatsuki, will explain more as the story goes on. PM or Review any questions or requests. Expect update within a week.**


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